Since you are talking Required Fuel, I am guessing that this is a Megasquirt application? 1000cc/700cc = 1.43, a 43 % increase in fuel flow rate. 5.6 ms/1.43 = 3.9 ms. The Req fuel calculator in Tuner Studio is working just fine and you need to polish up your math skills a bit.
If your configuration in Tuner Studio is correct, you can alter the size of your injectors, recalculate and apply the new value of Req Fuel, change the injector opening times and voltage sensitivity to match the new injectors and within reason you should not need to make any other changes to the Tuner Studio configuration settings. If the injector flow rates, injector opening times and voltage sensitivities were correct for both the 700 cc injectors and the 1000 cc injectors then you should not have to alter the other configuration settings. If you had errors in your original injector data then your other Tuner Studio settings will have been adjusted to make up for those errors. As such, even if you have correct data for the 1000 cc injectors you are putting them into a fudged configuration and you are starting all over. Same if you don't have correct data for the 1000 cc injectors.
Increasing the Req Fuel to 10.0 ms has the effect (everything else being unchanged) of reducing the calculated fuel pulse width. If you needed to increase Req Fuel / reduce your calculated fuel pulse width to get the car started, I am guessing that you were applying too much fuel during cranking with your original settings. Have you been logging any of these starts. Do you know what your cranking PW values were before you did the injector change and what they were after?
Putting in larger injectors increases the sensitivity to correct injector opening time and voltage sensitivity. If you have an error in the calculated fuel pulse width at idle because of incorrect injector opening time you have potentialy increased the magnitude of the error by 43 % with your new injectors. If you want the engine to start and idle well with large injectors you absolutely have to have the correct values for open time and voltage sensitivity for the injectors.
A Ve value of 90 in an idle cell in the fuel map is really odd. My car runs Ve values around 48 in the idle cells (MAP around 55, RPM 900) and if you use any of those generic Ve table generators you will typically get Ve values in the 40 - 50 range. This suggests to me that your configuration in Tuner Studio is off.